[gmx-developers] regd do_fnbf() non bonded interaction

[Anjan Raghunathan]

thanks Jason, that would really help.
   Sorry for this basic question, but I could not find atomtypes atructure,I guess you must have created that. 
   How do I find which atom is associated with which atom type number(other than traversing the whole lot of atoms in the topology structure and checking the name and type)?

thanks,
Anjan

---- Original message ----
>Date: Thu,  5 Feb 2004 12:42:07 -0500
>From: Jason DeJoannis <jdejoan at emory.edu>  
>Subject: Re: [gmx-developers] regd do_fnbf() non bonded interaction  
>To: gmx-developers at gromacs.org
>
>Hi Anjan,
>
> See my postings from a couple months ago. I modified do_force() to
>include such a mutation. But so far complex (i.e. polyatomic) mutations
>are beyond me. Here is a sample monte carlo mutation:
>
>bool do_atom_mutation(int *seed, int i, int tj, 
>             t_topology *top, t_mdatoms *mdatoms,
>             rvec x[], t_forcerec *fr, real beta, 
>             t_atomtypes *atypes)
>{
> /* I've omitted the calculation of the acceptance probability mut_acc */
>
>  if (rando(seed) < mut_acc) {  /* accept the mutation */
>    mass_change = atypes->mass[tj] - top->atoms.atom[i].m;
>    top->atoms.atom[i].type = tj;
>    top->atoms.atom[i].m    = atypes->mass[tj];
>    top->atoms.atom[i].q    = atypes->charge[tj];
>    mdatoms->typeA[i]       = tj;
>    mdatoms->massA[i]       = atypes->mass[tj];
>    mdatoms->chargeA[i]     = atypes->charge[tj];
>    mdatoms->tmass         += mass_change;
>    mdatoms->invmass[i]     = 1.0/atypes->mass[tj];
>    mdatoms->massT[i]       = atypes->mass[tj];
>    top->atoms.atomname[i]  = atypes->atomname[tj];
>    top->atoms.resname[i]   = atypes->resname[tj];
>    return(TRUE);
>  }
>  else
>    return(FALSE);
>}
>
>  Any suggestions for polyatomic mutation, eg: H2O->NH3  ??
>
>---
>Jason de Joannis, Ph.D.
>Chemistry Department, Emory University
>1515 Pierce Dr. NE, Atlanta, GA 30322
>Phone: (404) 712-2983
>Email: jdejoan at emory.edu
>http://userwww.service.emory.edu/~jdejoan
>
>
>
>> Date: Wed, 4 Feb 2004 09:22:18 -0600
>> From: Anjan Raghunathan <araghuna at uiuc.edu>
>> Subject: Re: [gmx-developers] regd do_fnbf() non bonded interaction
>> calculation
>> To: gmx-developers at gromacs.org
>> Reply-To: gmx-developers at gromacs.org
>> 
>> Hi,
>>    Thanks for the suggestion.Will go with it.
>>  One more Q...
>> Suppose I need to change the particle itself that is being simulated during
>> the run of the simulation.
>> For example, suppose potassium is being simulated in a fluid and after a
>> particular time or region I'd like to make it some other particle say
>> sodium.(Though this is artificial I really would like to know if this
>> procedure is possible).
>>    So basically, how can I change the LJ parameters and the charge of the
>> particle inside the code in GROMACS?
>> 
>> thanks,
>> Anjan
>> 
>> 
>
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_______________________________________

Anjan V. Raghunathan
Graduate Research Assistant
Computational Electronics Group
3213 Beckman Institute,
Univ. of Illinois at Urbana-Champaign.

E-mail:araghuna at uiuc.edu 
Off: 217-244-1964
Res: 217-355-5418